On one side of the debate on the history of the California missions are the state’s educational curriculum, the state park system, countless chambers of commerce and tourist boards, the Catholic Church, and generations of Californians steeped in the imagery and mythos of the state’s creation story.

On the other side of the debate is Elias Castillo.

Castillo, a three-time Pulitzer Prize-nominated journalist, has written a new book called “A Cross of Thorns” (Craven Street Books) that presents the case that the establishment of the 21 missions along the California coast in the 18th century spearheaded by Franciscan priest Junipero Serra was nothing less than an act of enslavement and genocide against the indigenous people of California.

“The average person has no idea what really happened,” said Castillo. “My goal was to compile irrefutable evidence, drawn directly from the words of Serra (and others at the time) and to describe in detail what happened to the native people in the missions.”

The book is being released just as the Catholic Church is poised to canonize Serra. Castillo said that the timing is coincidental, but his book does keep alive the controversy behind the sainthood of California’s most famous religious figure.

Pope Francis, who will make official Serra’s canonization during a September visit to the U.S., has called Serra “the evangelizer of the West in the United States.” Some historians, such as Gregory Orfalea, the author of the Serra history “Journey to the Sun,” say that Serra was a conscientious defender of California’s Indian population, and that his virtues clearly outweigh his sins.

Castillo insists otherwise, painting a picture of the mission settlements as a vanguard of European religious and cultural imperialism that annihilated the Indians’ own way of life, enslaving them and decimating their original population by up to 90 percent.

“The Franciscans took it upon themselves to brutalize the Indians, and to rejoice in their deaths,” he said. “For them, the earthly life was no concern. They simply wanted the souls of these Indians, so they baptized them and when they died, from disease or beatings or whatever, they were going to heaven, which was a cause of celebration.”

As the church’s leader in the settlement of what was then called “Alta California” in the late 1700s, Serra, said Castillo, was more than a figurehead.

“He set the policies of how they should consider the Indians,” he said. “And that’s a big question looming over Serra: Was he psychopathic? And it seems that he was.”

Drawing from archival government and church sources, and first-hand accounts of Serra himself, other friars and European visitors, “Cross of Thorns” documents various methods the church used to intimidate and control Indian subjects, from putting people in irons and stocks, to regular whippings and beatings.

“Once they were baptized, they could never leave the missions,” he said. “And neither could their children, or their children’s children. You have to describe it as slavery. No question about it. And the lack of immunity from European diseases, the stress from the abuse and the beatings, and the malnutrition – all this visited upon these poor Indians who had established a sustainable and complex civilization forced to abandon their beliefs, their faith, their way of life.”

The mission period lasted until the mid 1830s, when the newly independent government of Mexico decommissioned the missions, kicking off a brief period of liberal reforms that promised the Indians some control over their lives again. Then gold was discovered at Sutter’s Mill and everything changed again for the remnants of California’s native people.

“The missions,” Castillo writes in “A Cross of Thorns,” “where thousands of Indians remain buried in unmarked mass graves, were resurrected in the 1890s and 1900s and rebuilt as monuments to a concocted past that featured a loving, cooperative relationship between the friars and the Indians. Many California leaders, either ignorant of the truth or choosing to ignore what had happened, joined in this duplicity.”